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Techniques for Visualization of Anatomy and Function from MRI

Techniques for Visualization of Anatomy and Function from MRI. Steve Pieper, PhD VizBi 2010 Heidelberg. Outline. Motivation Standard Clinical MRI Visualization Research Imaging Registration Segmentation and Parcellation Functional Imaging Applications and Open Issues.

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Techniques for Visualization of Anatomy and Function from MRI

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  1. Techniques for Visualization of Anatomy and Function from MRI Steve Pieper, PhD VizBi 2010 Heidelberg

  2. Outline • Motivation • Standard Clinical MRI Visualization • Research Imaging • Registration • Segmentation and Parcellation • Functional Imaging • Applications and Open Issues

  3. Example: Morphometry Group Statistics • Regional Cortical Thickness Correlation with Aging and Cognitive Impairment • Greater Sensitivity than Clinical Tests • Localize Disease within Brain Anatomy • Impact of Treatment on Imaging Biomarkers Fischl, Greve, et al - MGH

  4. Example: Multimodality Image Guided Neurosurgery • Detailed Pre-Operative Model • Registered to Tracked Instruments • Superimposed on Intraoperative MRI • Extracted Anatomy and Function • Roadmap for Surgical Decision Making • What is the Best Surgical Approach to Preserve Function? Golby, Kikinis, Lemaire, BWH Neurosurgery

  5. MRI Context • MRI: Typically Volumetric at ~1mm Resolution • Unlike CT, No Physical Units for MR • Contrast Determined by Scan Protocol • Much of clinical MRI is pattern recognition • Seeing things that “don’t look right” • Anatomical Conventions • Like Maps having North at the Top • Axial (Transverse), Sagittal, Coronal • Analysis Results • Spatially Localized Data • Often visualization is used as a ‘reasonableness check’ on the automated calculations Wikipedia

  6. Basic Clinical Visualization • Window/Level • Corner Annotations • Pseudocolor • Mosaic/Lightbox • Cine

  7. 3D Clinical Visualization • Ray Casting Through Volume • Summation (Simulated X-Ray) • MIP (Maxiumum Intensity Projection) • SSD (Shaded Surface Display) • Color Transfer Function and Opacity Transfer Function • Pseudocolor + Gradient Lighting • Less Applicable for MRI than CT • Reference Labels for Standard Views • Left/Right, Anterior/Posterior, Inferior/Superior MR Angiogram MIP from Siemens Leonardo Workstation

  8. MRI Contrast Enhancement • Vascular / Oral: Gadolinium, Iron Oxide, Manganese • Change MR Properties of Tissues • Dynamic Contrast Tissue Enhancement (4D) • Vascularized Tumor • Stroke Related Ischemia • Perfusion, Diffusion, Bloodflow • Mismatch Indicates Brain Tissue that May Recover Gilbert et al University of Wisconsin Gonzalez et al MGH

  9. Longitudinal Imaging (4D) • Volumes Acquired Over Multiple Visits • “Watchful Waiting” Prior to Intervention • Monitor Treatment (Multiple Sclerosis, Cancer, Lupus…) • Comparison View • Linked Cursors • Subtraction Imaging and Quantification Guttmann, Meier, Fedorov – BWH Miller - GE

  10. Registration • Intra-subject • Pre-Intra-Post Procedure • Longitudinal Tracking of Disease Progression • Inter-subject • Support Group Comparison (fMRI) • Map Anatomical Atlas to Individual • Degrees of Freedom (DOFs) • Rigid (Rotation + Translation) • Similarity (Rigid + Uniform Scale) • Affine (Rigid + Nonuniform Scale and Shear) • Polyaffine (Locally Affine Interpolation) • B-Spline (Cubic Displacement) • Vector Field Sota - BWH

  11. Registration Considerations • Registration is Typically an Ill-Posed Problem • Requires Nonlinear Optimization • Distortions, Anatomy, Pathology Means No Exact Correspondence • Multimodality Registration Requires Statistical Metric (e.g. Mutual Information) • When No “Right” Answer • Only What “Looks Right” or • What is Reproducible and Statistically Significant • Insight Toolkit (ikt.org) for Details and Software Registration Method FixedImage Metric Optimizer Ibanez - Kitware Interpolator MovingImage Transform

  12. Registration Visualization • Cross Fade / Toggle • Color / Skeleton Overlay • Checkerboard • Vector Fields

  13. Segmentation • Definition: Assignment of Anatomical Labels to Image Regions • Not an Exact Science • Anatomists Disagree • Definition Depends on Scale • Techniques • Intensity Driven: Function of Image Measurements • Thresholding is Most Common (Typically Bad for MRI) • Rule Based: • E.g. “Skin is always on the outside” • Obviously not always the case in clinical scans • Atlas Driven: Registration of Manually Labeled Data • Also difficult for clinical scans • Hybrid Approaches Typically Required • E.g. Expectation Maximization (EM) Pohl – IBM Kikinis, Shenton - BWH

  14. Segmentation Visualization • Label Map Overlay • Cross Fade / Toggle • Solid or Outline • 3D Surface Models • Leverage Commodity Graphics Cards • Material Properties, Lighting, Transparency…

  15. Parcellation • Functional or Anatomical Subdivisions (e.g. Cerebral Hemisphere Surface) • Obtained from Curvature and Landmarks on Surface • Flattened to Plane or Sphere for Tractability • Displayed Inflated to Show Sulci (Valleys) and Gyri (Ridges) Fischl et al - MGH

  16. Functional MRI • Blood Oxygen Level Dependent (BOLD) • Volume Time Series ~2mm Resolution • Activation Statistics Volume: Typically Generalized Linear Model (GLM) of • Hemodynamic Response Function (HRF) • Stimulus / Paradigm • Intensity Trends • Physiology • Motion… • Statistics Become Difficult • Noisy Data • Multiple Comparisons / Multiple Regressors • Detects Metabolism, not Neural Activity Directly Finger Tapping Plesniak, Liu - BWH

  17. fMRI Visualization • Statistics Volume • Multi Volume Rendering • Cortical Surface Map • Group Comparisons in Atlas Space (Spatial Normalization) • Group Contrasts (Left/Right, Schizophrenics/Normal Control, Active/Resting…) • Positive and Negative Correlations Plesniak, Liu – BWH Hernell – Linköpings U.

  18. Multi-Modality Imaging • Integrated Visualization of What is Known About the Subject • Anatomical Space as Common Coordinate System • Segmented Anatomy and Volume Rendering for Context • Statistics Volumes • Interactive Visualization (View, Visibility, Cropping, Slicing… ) • Image Guided Therapies Plesniak, Aucoin et al - BWH Jakab and Berenyi - University of Debrecen

  19. Group Comparisons • Visualization for MRI Data Mining • Images, Clinical Data, Demographics on Web Database • Target Population and Hypothesis Specify Batch Computation • Group Statistics Overlay on Inflated Cortical Surface of Atlas • Click to Get Scatter Plot of Subjects • Supports Alzheimer’s Disease Research • Anatomy Labels Linked to Web Resources and Journal Papers Morphometry BIRN Consortium

  20. Open Challenges in MRI Visualization • Stereo / Virtual Reality (VR) / Augmented Reality (AR) / Telepresence • No real traction in spite of significant investment • Probably due to lack of mainstream hardware • Dynamic multimodal volume rendering • Large volumes – CUDA vs. Cluster • Encode segmentation in transfer function • General Information Overload • Display of Uncertainty in Analysis Results • Many techniques require discretization

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